#-------------------------------------------------------------------------------
# Stage 2.3: NVE integration for Deposition for 500 ps with a timestep of 0.2 fs
#-------------------------------------------------------------------------------
group deposition_atoms_TMOS_1_1 id 135333 135334 135335 135336 135337 135338 135339 135340
8 atoms in group deposition_atoms_TMOS_1_1
group deposition_atoms_TMOS_1_1 id 135341 135342 135343 135344 135345 135346 135347 135348
16 atoms in group deposition_atoms_TMOS_1_1
group deposition_atoms_TMOS_1_1 id 135349 135350 135351 135352 135353
21 atoms in group deposition_atoms_TMOS_1_1
delete_atoms group deposition_atoms_TMOS_1_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 21 atoms, new total = 135395
molecule depositing_species_TMOS_1_1 deposition_TMOS_1_1.dat
Read molecule template depositing_species_TMOS_1_1:
1 molecules
0 fragments
21 atoms with max type 4
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region deposition_region_TMOS_1_1 block EDGE EDGE EDGE EDGE 900 1180 units box
group deposition_atoms_TMOS_1_1_1 id 135354 135355 135356 135357 135358 135359 135360 135361
8 atoms in group deposition_atoms_TMOS_1_1_1
group deposition_atoms_TMOS_1_1_1 id 135362 135363 135364 135365 135366 135367 135368 135369
16 atoms in group deposition_atoms_TMOS_1_1_1
group deposition_atoms_TMOS_1_1_1 id 135370 135371 135372 135373 135374
21 atoms in group deposition_atoms_TMOS_1_1_1
delete_atoms group deposition_atoms_TMOS_1_1_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 21 atoms, new total = 135374
molecule depositing_species_TMOS_1_1_1 deposition_TMOS_1_1_1.dat
Read molecule template depositing_species_TMOS_1_1_1:
1 molecules
0 fragments
21 atoms with max type 4
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region deposition_region_TMOS_1_1_1 block EDGE EDGE EDGE EDGE 900 1180 units box
group deposition_atoms_TMOS_2_1_1 id 135375 135376 135377 135378 135379 135380 135381 135382
8 atoms in group deposition_atoms_TMOS_2_1_1
group deposition_atoms_TMOS_2_1_1 id 135383 135384 135385 135386 135387 135388 135389 135390
16 atoms in group deposition_atoms_TMOS_2_1_1
group deposition_atoms_TMOS_2_1_1 id 135391 135392 135393 135394 135395
21 atoms in group deposition_atoms_TMOS_2_1_1
delete_atoms group deposition_atoms_TMOS_2_1_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 21 atoms, new total = 135353
molecule depositing_species_TMOS_2_1_1 deposition_TMOS_2_1_1.dat
Read molecule template depositing_species_TMOS_2_1_1:
1 molecules
0 fragments
21 atoms with max type 4
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region deposition_region_TMOS_2_1_1 block EDGE EDGE EDGE EDGE 900 1180 units box
group deposition_atoms_TMOS_3_1_1 id 135396 135397 135398 135399 135400 135401 135402 135403
8 atoms in group deposition_atoms_TMOS_3_1_1
group deposition_atoms_TMOS_3_1_1 id 135404 135405 135406 135407 135408 135409 135410 135411
16 atoms in group deposition_atoms_TMOS_3_1_1
group deposition_atoms_TMOS_3_1_1 id 135412 135413 135414 135415 135416
21 atoms in group deposition_atoms_TMOS_3_1_1
delete_atoms group deposition_atoms_TMOS_3_1_1
WARNING: Ignoring 'compress yes' for molecular system (src/delete_atoms.cpp:140)
Deleted 21 atoms, new total = 135332
molecule depositing_species_TMOS_3_1_1 deposition_TMOS_3_1_1.dat
Read molecule template depositing_species_TMOS_3_1_1:
1 molecules
0 fragments
21 atoms with max type 4
0 bonds with max type 0
0 angles with max type 0
0 dihedrals with max type 0
0 impropers with max type 0
region deposition_region_TMOS_3_1_1 block EDGE EDGE EDGE EDGE 900 1180 units box
uncompute thermo_temp
compute thermo_temp movable temp
thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
thermo ${Nthermo}
thermo 0
fix 1 movable nve
fix dlan subset_thermoset langevin 300 300 20.0 502832 tally yes
fix 2 movable ave/time 1 250000 250000 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy f_dlan file 2.3_averages.txt off 1
fix 3 movable ave/time 250 1 250 v_time c_thermo_temp c_thermo_press v_sysvol v_sysdensity v_etotal v_pe v_ke v_evdwl v_coulomb v_sxx v_syy v_szz v_syz v_sxz v_sxy f_dlan file 2.3_instantaneous.txt
fix 4 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix deposition_TMOS_1_1_1 deposition_atoms_TMOS_1_1 deposit 500 0 5000 3278197 region deposition_region_TMOS_1_1 mol depositing_species_TMOS_1_1 vz -0.030302007549477986 -0.037035787004917539 vx -0.05831624071892394 0.05831624071892394 vy -0.05831624071892394 0.05831624071892394 near 1.50 id next units box
fix deposition_TMOS_1_1_2 deposition_atoms_TMOS_1_1 nve
fix deposition_TMOS_1_1_1_1 deposition_atoms_TMOS_1_1_1 deposit 500 0 5000 901334 region deposition_region_TMOS_1_1_1 mol depositing_species_TMOS_1_1_1 vz -0.030302007549477986 -0.037035787004917539 vx -0.05831624071892394 0.05831624071892394 vy -0.05831624071892394 0.05831624071892394 near 1.50 id next units box
fix deposition_TMOS_1_1_1_2 deposition_atoms_TMOS_1_1_1 nve
fix deposition_TMOS_2_1_1_1 deposition_atoms_TMOS_2_1_1 deposit 500 0 5000 5212345 region deposition_region_TMOS_2_1_1 mol depositing_species_TMOS_2_1_1 vz -0.030302007549477986 -0.037035787004917539 vx -0.05831624071892394 0.05831624071892394 vy -0.05831624071892394 0.05831624071892394 near 1.50 id next units box
fix deposition_TMOS_2_1_1_2 deposition_atoms_TMOS_2_1_1 nve
fix deposition_TMOS_3_1_1_1 deposition_atoms_TMOS_3_1_1 deposit 500 0 5000 21 region deposition_region_TMOS_3_1_1 mol depositing_species_TMOS_3_1_1 vz -0.030302007549477986 -0.037035787004917539 vx -0.05831624071892394 0.05831624071892394 vy -0.05831624071892394 0.05831624071892394 near 1.50 id next units box
fix deposition_TMOS_3_1_1_2 deposition_atoms_TMOS_3_1_1 nve
dump trj all custom 50000 2.3.Trajectory.xyz id mol type q xs ys zs
fix trjE all ave/time 50000 1 50000 v_etotal v_pe v_ke file 2.3.energies.txt
dump trj_TMOS_1_1 deposition_atoms_TMOS_1_1 custom 50000 2.3.trajectory_1.xyz id mol type q xs ys zs
dump trj_TMOS_1_1_1 deposition_atoms_TMOS_1_1_1 custom 50000 2.3.trajectory_2.xyz id mol type q xs ys zs
dump trj_TMOS_2_1_1 deposition_atoms_TMOS_2_1_1 custom 50000 2.3.trajectory_3.xyz id mol type q xs ys zs
dump trj_TMOS_3_1_1 deposition_atoms_TMOS_3_1_1 custom 50000 2.3.trajectory_4.xyz id mol type q xs ys zs
timestep 0.2
run 2500000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 12, bins = 25 3 100
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c/kk, perpetual
attributes: half, newton off, ghost, kokkos_